Results

Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavitythrough a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the number of bonds that have entered the cavity.
To study polymer in...

Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, lambda, and exam...

In this study, we employ the discontinuous molecular dynamics simulation method to investigate the collapse properties of a single heteropolymer chain in an explicit solvent. Solvent density ρ, fraction of hydrophobic monomers n H (defined as the ratio of the number of hydrophobic monomers to the t...

Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that tr...

We have used Brownian dynamics simulations to study the dynamics of a bead-and-spring polymer subject to a flashing ratchet potential. To elucidate the role of hydrodynamic (HD) interactions, simulations were carried out for the cases where HD interactions are present and when they are absent. The a...

The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for ...

Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good solvent conditions. The dynamics of the polymer chain were investigated using an analysis of the time autocorrelation functions of the Rouse coordinates of t...

Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different versions of the model were employed, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbonded monomer-monomer interactions. ...

Molecular dynamics simulations are used to study the coil-globule transition for a system composed of a bead-spring polymer immersed in an explicitly modeled solvent. Two different versions of the model are used, which are differentiated by the nature of monomer-solvent, solvent-solvent, and nonbond...

We employ Molecular Dynamics simulations to study the phase behavior and equilibrium dynamics of a fully flexible Lennard-Jones chain immersed in a Lennard-Jones solvent at high solvent densities. The hydrophobicity of the model polymer is adjusted by varying the attractive component of either the m...

We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often studied in simulations. Specifically, we clarify the performanc...

We study the equilibrium behavior and dynamics of a polymer collapse transition for a system composed of a short Lennard-Jones (LJ) chain immersed in a LJ solvent for solvent densities in the range of rho=0.6-0.9 (in LJ reduced units). The monomer hydrophobicity is quantified by a parameter lambdais...

We employ off-lattice Monte Carlo simulations to study lateral diffusion in lipid-sterol bilayers using a two-dimensional model system which has been designed to simulate the experimental phase diagrams of both lipid-cholesterol and lipid-lanosterol systems. We focus on the effects of varying sterol...

We analyze the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading (ln N/N) corrections, the remaining free energy is found to depend linearly on 1/N. Extrapolating to the thermodynamic limit (N -->infinity), we estimate t...

Molecular dynamics simulations are used to study the equilibrium properties and collapse dynamics of a heteropolymer in the presence of an explicit solvent in two dimensions. The system consists of a single copolymer chain composed of hydrophobic (H) and hydrophilic (P) monomers, immersed in a Lenna...

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compre...

We use molecular dynamics simulations to study an entropy-driven collapse transition of a flexible polymer in a solvent. Monomers and solvent particles interact with a steeply repulsive soft-sphere potential. We consider a nonadditive potential system in which the effective diameter describing the s...

The anisotropic intermolecular forces responsible for the orientational ordering in liquid crystals are probed by comparing Monte Carlo (MC) simulations with experimental nuclear magnetic resonance (NMR) results for solutes in nematic liquid crystals. In a special liquid crystal mixture where all lo...